mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.968021762817626 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:140183058G>AN/A show variant in all transcripts IGV

HGNC symbol

PCDHA3

Ensembl transcript ID

ENST00000532566

Genbank transcript ID

NM_031497

UniProt peptide

Q9Y5H8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2276G>A
cDNA.2276G>A
g.2276G>A

AA changes

C759Y Score: 194 explain score(s)

position(s) of altered AA
if AA alteration in CDS

759

frameshift

known variant

Reference ID: rs2240694

database	homozygous (A/A)	heterozygous	allele carriers
1000G	717	1197	1914
ExAC	16867	-967	15900

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.04	0.922
	3.269	0.921
(flanking)	-0.355	0.194

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor increased	2278	wt: 0.37 / mu: 0.73	wt: TGTGCTCTGGAGAGG mu: TGTACTCTGGAGAGG	TGCT\|ctgg
Donor marginally increased	2268	wt: 0.2619 / mu: 0.2827 (marginal change - not scored)	wt: CAGCAGAGGGTGTGC mu: CAGCAGAGGGTGTAC	GCAG\|aggg
Donor increased	2281	wt: 0.60 / mu: 0.77	wt: GCTCTGGAGAGGGGT mu: ACTCTGGAGAGGGGT	TCTG\|gaga
Donor marginally increased	2280	wt: 0.9168 / mu: 0.9607 (marginal change - not scored)	wt: TGCTCTGGAGAGGGG mu: TACTCTGGAGAGGGG	CTCT\|ggag

distance from splice site

200

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

759

mutated

not conserved

759

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000032691

750

protein features

start (aa)	end (aa)	feature	details
719	950	TOPO_DOM	Cytoplasmic (Potential).	lost
734	894	REGION	6 X 4 AA repeats of P-X-X-P.	lost
774	777	REPEAT	PXXP 2.	might get lost (downstream of altered splice site)
799	802	REPEAT	PXXP 3.	might get lost (downstream of altered splice site)
832	835	REPEAT	PXXP 4.	might get lost (downstream of altered splice site)
873	876	REPEAT	PXXP 5.	might get lost (downstream of altered splice site)
891	894	REPEAT	PXXP 6.	might get lost (downstream of altered splice site)
923	930	COMPBIAS	Poly-Lys.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2475 / 2475

position (AA) of stopcodon in wt / mu AA sequence

825 / 825

position of stopcodon in wt / mu cDNA

2475 / 2475

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

1 / 1

chromosome

strand

last intron/exon boundary

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

2475

coding sequence (CDS) position

2276

cDNA position
(for ins/del: last normal base / first normal base)

2276

gDNA position
(for ins/del: last normal base / first normal base)

2276

chromosomal position
(for ins/del: last normal base / first normal base)

140183058

original gDNA sequence snippet

GCAGAGGCAGCAGAGGGTGTGCTCTGGAGAGGGGTTGCCCA

altered gDNA sequence snippet

GCAGAGGCAGCAGAGGGTGTACTCTGGAGAGGGGTTGCCCA

original cDNA sequence snippet

GCAGAGGCAGCAGAGGGTGTGCTCTGGAGAGGGGTTGCCCA

altered cDNA sequence snippet

GCAGAGGCAGCAGAGGGTGTACTCTGGAGAGGGGTTGCCCA

wildtype AA sequence

MLFSWREDPG AQCLLLSLLL LAASEVGSGQ LHYSVSEEAK HGTFVGRIAQ DLGLELAELV
PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVE
VEVKDINDNA PVFPMAVKNL FISESRQPGS RFSLEGASDA DIGTNSLLTY SLDSTEYFTL
DVKRNDEEIK SLGLVLKKNL NREDTPKHYL LITAIDGGKP ELTGTTQLKI TVLDVNDNAP
AFERTIYKVR LLENAPNGTL VVTVNATDLD EGVNKDIAYS FNTDMSADIL SKFHLDPVNG
QISVKGNIDF EESKSYEIQV EATDKGNPPM SDHCTVLLEI VDINDNVPEL VIQSLSLPVL
EDSPLSTVIA LISVSDRDSG VNGQVTCSLT PHVPFKLVST FKNYYSLVLD SPLDRESVSA
YELVVTARDG GSPSLWATAS VSVEVADVND NAPAFSQSEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLMPRV GGIGGAVSEL VPRSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPGTGGARI PFRVGLYTGE ISTTRALDEV DAPRHRLLVL VKDHGEPSLT
ATATVLVSLV ESGQAPKASS QASAGATGPE AALVDVNVYL IVAICAVSSL LVLTLLLYTA
LRCSAPPTEG DCGPGKPTLV CSSAVGSWSY SQQRQQRVCS GEGLPKTDLM AFSPSLPPCP
ISRDREEKQD VDVDLSAKVS NFYLFFPKCL CFSFLNVSTP LEIH*

mutated AA sequence

MLFSWREDPG AQCLLLSLLL LAASEVGSGQ LHYSVSEEAK HGTFVGRIAQ DLGLELAELV
PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVE
VEVKDINDNA PVFPMAVKNL FISESRQPGS RFSLEGASDA DIGTNSLLTY SLDSTEYFTL
DVKRNDEEIK SLGLVLKKNL NREDTPKHYL LITAIDGGKP ELTGTTQLKI TVLDVNDNAP
AFERTIYKVR LLENAPNGTL VVTVNATDLD EGVNKDIAYS FNTDMSADIL SKFHLDPVNG
QISVKGNIDF EESKSYEIQV EATDKGNPPM SDHCTVLLEI VDINDNVPEL VIQSLSLPVL
EDSPLSTVIA LISVSDRDSG VNGQVTCSLT PHVPFKLVST FKNYYSLVLD SPLDRESVSA
YELVVTARDG GSPSLWATAS VSVEVADVND NAPAFSQSEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLMPRV GGIGGAVSEL VPRSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPGTGGARI PFRVGLYTGE ISTTRALDEV DAPRHRLLVL VKDHGEPSLT
ATATVLVSLV ESGQAPKASS QASAGATGPE AALVDVNVYL IVAICAVSSL LVLTLLLYTA
LRCSAPPTEG DCGPGKPTLV CSSAVGSWSY SQQRQQRVYS GEGLPKTDLM AFSPSLPPCP
ISRDREEKQD VDVDLSAKVS NFYLFFPKCL CFSFLNVSTP LEIH*

speed

1.12 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project